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switch from papaya to brainsprite in plotting.view_stat_map #1766

Merged
merged 109 commits into from
Nov 10, 2018
Merged

switch from papaya to brainsprite in plotting.view_stat_map #1766

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45bf7fa
Merge pull request #1 from nilearn/master
pbellec Sep 28, 2018
7188176
Switch from papaya to brainsprite in plotting.view_stat_map
pbellec Sep 28, 2018
89215ef
Switch from papaya to brainsprite in plotting.view_stat_map, part 2
pbellec Sep 28, 2018
c1ec5ab
1. Switched to png background image, because jpg not always supported…
pbellec Sep 29, 2018
3a0602c
Fixing typo in URL.
pbellec Sep 29, 2018
de80f48
Making code to conform to PEP8 standards.
pbellec Sep 29, 2018
c4e6be3
Changed control of the size of iframe from width (px), height (px) to…
pbellec Oct 6, 2018
1917831
Set the aspect ratio of the viewer to 44% (heigth / width).
pbellec Oct 6, 2018
a071dae
Fixing PEP8 compliance.
pbellec Oct 6, 2018
595ea34
Re-ordered imports (general > science > neuroimaging > local)
pbellec Oct 9, 2018
1f8b5d0
Bug fix in the import + hard-coded n_colors
pbellec Oct 9, 2018
6033d93
Turned plotting.html.stat_map.save_sprite into a private function _sa…
pbellec Oct 9, 2018
4be505f
Fix possible rounding error in thresholding a color map.
pbellec Oct 10, 2018
f17cb3b
1. Started making code more modular. 2. Masking image prior to resamp…
pbellec Oct 10, 2018
48ad18f
Modularized the code a bit. WIP.
pbellec Oct 11, 2018
c4e5983
More modularity. Also fixed the "grey voxel artefact".
pbellec Oct 11, 2018
0938e83
Got rid of intermediate parameter dump.
pbellec Oct 11, 2018
b2a07e8
modularization refactoring complete.
pbellec Oct 11, 2018
57c7631
Fixed all flake8 warnings.
pbellec Oct 11, 2018
92d7d67
Added support for fill value in resampling tools.
pbellec Oct 14, 2018
542e5dc
More modularity, and fixed resampling bug.
pbellec Oct 14, 2018
e5e908a
Updated the version of jquery to the one on nilearn's master, and fix…
pbellec Oct 18, 2018
afe5ade
Reverted the size of iframe to fixed width / height.
pbellec Oct 18, 2018
736eb5f
Transfered the generation of cmap with threshold to cm.py. Simplified…
pbellec Oct 18, 2018
d974117
Turned cm.threshold_cmap into a private function cm._threshold_cmap.
pbellec Oct 18, 2018
a2c848f
Merge branch 'master' of https://github.com/nilearn/nilearn into nile…
pbellec Oct 18, 2018
1b532cf
Fixed error that happened during the merge.
pbellec Oct 18, 2018
4a0cc6a
Merge branch 'nilearn-master'
pbellec Oct 18, 2018
83d3b75
Try `reorder_img` before resampling to diagonal affine.
pbellec Oct 18, 2018
84794a9
Adapting the size of the viewer to the actual aspect ratio of the image.
pbellec Oct 18, 2018
a103eb1
Fix previous commit: test properly if affine is diagonal, positive & …
pbellec Oct 18, 2018
1130e45
Renamed the `file` varible to a more explicit `bytesio_png`.
pbellec Oct 18, 2018
5460550
1. Use Template library to populate the html template. 2. Modularize …
pbellec Oct 19, 2018
cbf6d3a
Getting rid of `resample_to_isotropic_affine`, it's redundant with `r…
pbellec Oct 19, 2018
b6b9600
Added doc explaining the logic of _save_sprite.
pbellec Oct 19, 2018
625aac7
Got rid of un-necessary escaping.
pbellec Oct 19, 2018
20daa71
Now passes the flake8 test.
pbellec Oct 19, 2018
33702a1
Suppressing the _encode_nifti and _decode_nifti tests.
pbellec Oct 19, 2018
88ec48e
Added support for threshold of the form "90%".
pbellec Oct 19, 2018
518acef
1. Fixed a problem with admissible warnings. 2. Added DeprecationWarn…
pbellec Oct 19, 2018
fa5c4c1
Fixed flake8 warnings.
pbellec Oct 20, 2018
95b1616
Fixed flake8 warning.
pbellec Oct 20, 2018
fd134f1
Adding tests for 4D images with 1 time frame.
pbellec Oct 20, 2018
234110e
Replaced encodebytes for encodestrings, for python 2 compatibility.
pbellec Oct 20, 2018
15e95ea
Reverted back from html to cgi, for python2 compatibility.
pbellec Oct 20, 2018
0b3999c
Addressed some of @jeromedockes' comments.
pbellec Oct 20, 2018
f7ced11
Improved the syntax of one of the tests, following @jeromedockes' sug…
pbellec Oct 20, 2018
6a8a026
Switched from a `symmetric_cbar` argument to `symmetric_cmap`.
pbellec Oct 21, 2018
ffb3c62
Reverted all changes to cm.py. No need for _threshold_cmap anymore.
pbellec Oct 21, 2018
5e41871
Reverted display.py to the master version, as there is no use anymore…
pbellec Oct 21, 2018
278f138
Got rid of a deprecation warning.
pbellec Oct 21, 2018
23c0208
Added doc on vmax and symmetric_cmap
pbellec Oct 21, 2018
a1b20a2
Fixes rounding issues in `cut_coords`. Better labels for the colorba.
pbellec Oct 21, 2018
3399686
Added a test for _data2sprite
pbellec Oct 22, 2018
3c1cf41
Check that vmax is smaller than vmin, throw an error otherwise.
pbellec Oct 22, 2018
19252dd
test for _get_vmin_vmax
pbellec Oct 22, 2018
365005c
FIxed issue with matlib.repmat by switching to tile, following a sugg…
pbellec Oct 23, 2018
46251f3
Voxel that do not pass the threshold are now associated with a value …
pbellec Oct 23, 2018
c9b2d2a
Support threshold=None in _threshold_data
pbellec Oct 23, 2018
45262d7
Added a test for _threshold_data
pbellec Oct 23, 2018
0750692
PEP8 compliance + test_threshold_data will now actually run.
pbellec Oct 23, 2018
7dec3f5
PEP8 compliance.
pbellec Oct 23, 2018
0b39359
Fixing python2 compatibility and making code more clean/concise, than…
pbellec Oct 23, 2018
bbb3cbe
Forgot imports to assert warning / errors.
pbellec Oct 23, 2018
90b1974
Added a test for html_stat_map._get_cut_slices
pbellec Oct 23, 2018
a87bbcc
Added `n_colors` as parameter for _save_cm, because it is useful for …
pbellec Oct 24, 2018
7fc145f
New tests covering _save_sprite, _save_cm, as well as _bytesIO_to_base64
pbellec Oct 24, 2018
46f3111
Simplified a bit the test of base64 encoding to avoid errors in pytho…
pbellec Oct 25, 2018
b270186
Added a function `_sanitize_cm` to remove duplicate colors.
pbellec Oct 25, 2018
b94172c
Fixed back the centering of vmin / vmax in the colorbar.
pbellec Oct 25, 2018
249e078
Added a test for _sanitize_cm
pbellec Oct 25, 2018
f5cc4b3
Added an optional argument in _sanitize_cm to control the number of c…
pbellec Oct 25, 2018
fdc581a
A test for `_mask_stat_map`.
pbellec Oct 25, 2018
d714356
New test for load_bg_img.
pbellec Oct 25, 2018
bc5cc64
New test for `_resample_stat_map`.
pbellec Oct 26, 2018
8c15fc6
Added minimal testing for `_json_sprite`.
pbellec Oct 26, 2018
1890f7f
A new test for `_get_size_sprite`.
pbellec Oct 26, 2018
129acb1
Re-ordering tests to match order of functions in html_stat_map.
pbellec Oct 26, 2018
51d8834
More modularity. Codebase should be modular enough now.
pbellec Oct 26, 2018
3dfda7c
Moving code around for a better progression.
pbellec Oct 26, 2018
b48547e
New test for `_build_sprite_data`.
pbellec Oct 26, 2018
e33bafa
Avoid to directly change the colormap object.
pbellec Oct 26, 2018
b75e3ae
A new test for `_html_brainsprite`.
pbellec Oct 26, 2018
1f39f1c
Merge master
pbellec Oct 26, 2018
f59f078
Finish to merge master.
pbellec Oct 26, 2018
f993952
PEP8 compliance.
pbellec Oct 26, 2018
39e2872
Correct encoding tags for images.
pbellec Oct 27, 2018
b9b6e08
1. remove variable names with png. 2. force the colormap image to float.
pbellec Oct 27, 2018
eea8f93
Improve the docstring for the viewer.
pbellec Oct 29, 2018
63e3165
Removed () following `assert`. Added some error messages for failed t…
pbellec Oct 31, 2018
650b0c9
Added a test that `_get_vmin_vmax` works properly with NaNs in the data.
pbellec Oct 31, 2018
36757c2
A bunch of improvements, mostly on naming and docstring.
pbellec Oct 31, 2018
94b0f28
Updating brainsprite.js to fix a rounding error for `cut_coords` that…
pbellec Nov 4, 2018
930912f
Updated doc / screenshot from the papaya viewer to the brainsprite vi…
pbellec Nov 4, 2018
b1b92a5
The screenshot for view_stat_map using brainsprite.
pbellec Nov 4, 2018
742f03b
Bug fix in the doc.
pbellec Nov 4, 2018
9f87950
Use _utils.compat to deal with python2/3 compatibility.
pbellec Nov 5, 2018
716ebbe
Some docs improvement, following up on @KamalakerDadi's suggestions.
pbellec Nov 5, 2018
91f622b
Added `_encodbytes`, mapping to `base64.encodebytes` in python 3 and …
pbellec Nov 5, 2018
0aa1576
Using `_utils.compat._encodebytes` instead of local import for python…
pbellec Nov 5, 2018
f50c915
Added a `See Also` section to `view_stat_map`.
pbellec Nov 5, 2018
a1e344e
Improving doc and comments, thanks to @KamalakerDadi's feedback.
pbellec Nov 5, 2018
6a73df2
Getting rid of _get_vmin_vmax, which is not used.
pbellec Nov 5, 2018
3923b1d
Improved error message when improper cut_coords is provided.
pbellec Nov 5, 2018
e9defb4
Disable `value` when `colorbar=False` in `view_stat_map`.
pbellec Nov 5, 2018
a816107
Added brief summary of the PR in whats_new.rst
pbellec Nov 6, 2018
69d2c6c
Merge branch 'master' of https://github.com/nilearn/nilearn into nile…
pbellec Nov 6, 2018
4bae919
Merge branch 'nilearn-master'
pbellec Nov 6, 2018
59d28b2
fix doc line too long.
GaelVaroquaux Nov 9, 2018
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1 change: 1 addition & 0 deletions nilearn/plotting/data/README.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,4 @@ js/
surface-plot-utils.js : helpers for nilearn plots
plotly-gl3d-latest.min.js : plotly library (https://plot.ly/javascript/getting-started/)
jquery.min.js : jquery library (https://jquery.com/)
brainsprite.min.js : brainsprite library (https://simexp.github.io/brainsprite.js)
154 changes: 33 additions & 121 deletions nilearn/plotting/data/html/stat_map_template.html
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1 change: 1 addition & 0 deletions nilearn/plotting/data/js/brainsprite.min.js
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